Wednesday, 14 November 2012

Glycogen Synthase Kinase 3 (GSK3) and Glycogen Synthase (GS) - the phosphorylation equilibrium

This one causes students problems every year - the relationship between Glycogen Synthase Kinase 3 (GSK3) and Glycogen Synthase (GS), and their phosphorylation states and activity.

Blog Post Bonus: Download a PDF of this blog post for your class notes.
If you look at insulin signalling overall:

Is

You will see that activated protein kinase B (activated by phosphorylation) phosphorylates and inactivates GSK3. This means that GSK3 can no longer phosphorylate its substrate, GS.
Now, GS, when phosphorylated, is inactive. Hence, as GSK3 is no longer active (as it is phosphorylated) it cannot phosphorylate GS and inactivate it, therefore GS remains un-phosphorylated and therefore active so it can make glycogen.

Gsk3

The key to understanding this is that phosphorylated (inactive) and un-phosphorylated (active) forms of GS are in a state of equilibrium and that the kinase, GSK3, drives the equilibrium to the right (inactive) in the figure below, whereas the phosphatase (which removes the phosphate) drives the equilibrium to the left (active). Therefore, if you inhibit the action of the kinase (GSK3) the net result is more un-phosphorylated GS, hence more glycogen is made, which is just what we want…

Phosphate copy

One key thing to keep in mind is that the phosphorylation of a protein can cause it to become activate or inactive. It all depends on the protein.

Blog Post Bonus: Download a PDF of this blog post for your class notes.

Sunday, 4 November 2012

How do I submit work for plagiarism scanning using Blackboard?

Submitting work for plagiarism scanning using Blackboard is fairly straight forward and easy to do.
  1. Go to the module for which you wish to submit the work.
  2. Click on the link that says 'TurnItIn Submissions' in the lefthand menu.

Screen Shot 2012 11 04 at 12 04 29

  1. On the next page you will see a link that is relevant to your work. Click on it.

Screen Shot 2012 11 04 at 12 04 51

  1. You should now be on a screen that shows the upload system.


  1. Click the Submit button.
  2. You should now be on the first page (of 3) of the submission process. You name should already be filled in, however, the title will not be complete, and you need to enter one. You should also note the rules regarding the size (less than 400 pages, and less than 20 MB) and the file formats that can be submitted.

Screen Shot 2012 11 04 at 12 05 51

  1. Next, click the 'Choose File' button and navigate to, and select, your file for upload (see above screen shot).
  2. Finally, click the 'Upload' button and wait for the file to load.

Screen Shot 2012 11 04 at 12 05 59

  1. Once the file has been uploaded you should be in part 2 (of 3) of the submission process. This page can be used to review the file and for you to check you have selected the correct file in step 7. If the file is correct, click 'Submit'.

Screen Shot 2012 11 04 at 12 06 10

Screen after clicking submit:


  1. If the submission has been successful you should then see the following screen which confirms your work has been successfully uploaded.

  1. Finally, you can double check the work has been uploaded by going to 'My Grades' for the module. If the work has uploaded you should see an exclamation mark. This means the work has uploaded, but has not yet been marked.
Finally, below, is a short video walking you through the process.

Saturday, 20 October 2012

Calculating Percentage Solutions

For some reason percentage solution calculation cause students some problems. However, hopefully, once you have been through this blog post you should have a good understanding of percentage solutions, and how to do the calculations.

If you want to practice your 'science maths' than have a look at: Maths4Biosciences.com


Blog Post Bonus: Download a PDF for your class notes on percentage solution calculations.
If you are having problems with percentage solution calculations then you might like to check out the Percentage Solutions course over at the Maths4Biosciences School on Fedora

What are percentage solutions?

A percentage solution is an amount or volume of something per 100 ml or 100 g of a solution. It is as simple as that. It is a percentage.

Why are they used?

Percentage solutions are just a convenient and easy way to record solution concentrations. One advantage of percentage solutions is that you don’t need to know anything about the compound in terms of molecular weight as all you need is the percentage of the required solution.

Why are their three types of percentage solutions?

This is slightly difficult to explain. However, there are three types of percentage solution:
  • Percentage weight by volume (w/v)
  • Percentage volume by volume (v/v)
  • Percentage weight by weight (w/w)
The percentage weight by volume (w/v) is the number of grams of compound per 100 ml of solution. This type of percentage solution tends to be used when describing the amount of some powder made up in a solution. So, for example, 5 g of a powder made up to a final volume of 100 ml would be a 5% (w/v) solution. Likewise, 2.5 g of powder made up to 50 ml would also be a 5% (w/v) solution as you would have 5 g in 100 ml.

The percentage volume by volume (v/v) is the number of ml of some liquid per 100 ml of the solution. This type of percentage solution is usually used to describe a solution that is made by mixing two liquids. So, for example, 5 ml of a liquid made up to a final volume of 100 ml would be a 5% (v/v) solution. Likewise, 2.5 ml of a liquid made up to 50 ml would also be a 5% (v/v) solution as you would have 5 ml in 100 ml.

Blog Post Bonus: Download a percentage solution calculations spreadsheet
Finally, the percentage weight by weight (w/w). This one is a little more difficult to understand, but the principles as explained above are still true. A percentage weight by weight (w/w) solution can be a weight of a powder or a liquid made up in a solution to a final weight of the solution. So, for example, 5 g of a powder (or a liquid) made up in a solution that has a final weight of 100 g would be a 5% (w/w) solution. Likewise, 2.5 g of a liquid or powder made up to give a solution that weighed 50 g would also be a 5% (w/w) solution as you would have 5 g of the powder or liquid in 100 g of a solution.



If you are having problems with percentage solution calculations then you might like to check out the Percentage Solutions course over at the Maths4Biosciences School on Fedora

Blog Post Bonus: Download a PDF for your class notes on percentage solution calculations.

Tuesday, 16 October 2012

BGM3001:BMS3011 - lecture movies - 3d Structure of the GDP G-protein alpha subunit

The movie below shows the 3d structure of a guanosine diphosphate (GDP) bound G protein alpha-subunit.

Gdp alpha

The small green molecule in the middle is the bound GDP.

http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1TAG

BGM3001:BMS3011 - lecture movies - Bovine Rhodopsin

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

However, the crystal structure of bovine rhodopsin shows that the seven transmembrane spanning domains actually form a tight core

Bovine rhodopsin

J. Mol. Biol. (2004) 342, 571–583 http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1U19

BGM3001:BMS3011 - lecture movies - 3d Structure - β2AR-T4L

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

Which shows a receptor with the N-terminal outside the cell, seven transmembrane spanning domains, 3 exoloops, 4 cytoloops and a C terminal inside the cell.
However, it is actually more compact with the seven transmembrane spanning domains forming a tight core.

Beta2AR

Lower part = T4-lysozyme in place of cyto 3 Small green molecules = cholesterol; can just make out bound ligand in pocket
Science. 2007 318(5854): 1258–1265. http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2RH1

BGM3001:BMS3011 - lecture movies - αGs and Adenylyl Cyclase

The following animation shows αGs interacting with adenylyl cyclase.

Alpha adenylyl cyclase small

The animation is also available as a slightly larger video....

BGM3001:BMS3011 - lecture movies - GPCR movement of TM3 and 6

I have been asked for access to a number of the movies I used in the lectures.

The following animation shows the proposed movements of transmembrane spanning domains 3 and 6 for rhodopsin and β2 adrenergic receptor.

3 6 rotation

It should be noted that other GPCR may use different methods.

Monday, 15 October 2012

How do I get my marks and feedback on Blackboard

A number of the class have asked me how they can get their marks and feedback successfully on Blackboard.

The following short video explains how you can get your marks and feedback on modules that I teach on, and which have assessment (set by me) on Blackboard.

How do I know if I have submitted successfully on Blackboard?

A number of the class have asked me how they can check that they have successfully submitted work on Blackboard.

The following video explains how you can check on modules that I teach on, and which have assessment (set by me) on Blackboard.